Biomics

The year 2025 marks two anniversaries in connection with DNA sequencing in general and plant genomes in particular. So, 50 years ago, a relatively fast DNA sequencing method was developed, called the "plus/minus" method, which was soon replaced by two other even faster methods. The separation of sequencing reaction products by high-voltage gel electrophoresis became common to them all. Three decades later, non-electrophoretic methods had to be developed to increase the productivity of DNA sequencing, and many such methods appeared. At the same time, their improvement continues and new ones are being developed. 25 years ago, the first plant (nuclear) genome of the model plant Arabidopsis thaliana was sequenced, which was characterized by a mosaic assembly of paired chromosome fragments. The chloroplast and mitochondrial genomes of Arabidopsis were sequenced one year and three years earlier, respectively. It was only many years later that a diploid genome with phased haplotype assembly was sequenced for Arabidopsis and a nuclear pangenome was composed which must replace the obsolescent reference genomes. At the same time, neither the panplastome nor the panmitogenome for this model plant species, which is Arabidopsis, has yet been composed. However genomics should, in fact, turn into pangenomics, including relying on knowledge of haplotypes, since the concept of the reference genome has already outlived itself and it can be metaphorically compared to a single street lamp illuminating only a small space around beyond which nothing is visible, whereas the pangenome carries information about the full pool of genes characteristic of for a specific type. Really, a plant cell is controlled by a triad of nuclear, mitochondrial, and chloroplast genomes, and they all need to be sequenced, including taking into account intraspecific DNA polymorphism.

DNA, sequencing, genome, reference genome, quasi-genome, pangenome, super-pangenome, T2T genome, diploid genome, phased genome, haplotype-resolved genome, pan-plastome, pan-mitogenome, plant genomic triad

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